Fig. 1. CRISPRi screens identify lncRNA genes that modify cell growth.
(A) Schematic of CRISPRi library design strategy. Three lncRNA annotation
sets were merged, prioritized by expression in the indicated cell lines, and
targeted by 10 sgRNAs per TSS using the hCRISPRi-v2.1 algorithm. Heat
map represents expression as z-score of FPKM within each cell line (see fig.
S1 for TPM values). (B) Schematic of growth screens performed in seven
different cell lines, and formula for calculation of the growth phenotype (g).
(C) Scatterplot of sgRNA phenotypes from two independent replicates
of a CRISPRi screen performed in iPSCs. (D) Volcano plot of gene g and

P value. Screen replicates were averaged, and sgRNAs targeting the same
gene were collapsed into a growth phenotype for each gene by the average
of the three top-scoring sgRNAs by absolute value and assigned a P value
by the Mann-Whitney test of all 10 sgRNAs compared to the nontargeting
controls. Negative control genes were randomly generated from the set of
nontargeting sgRNAs; dashed lines represent a threshold for calling hits by
screen score (see supplementary materials). Neighbor hits are not displayed
for clarity (see fig. S3, A and B). (E) Summary table of all CRISPRi growth
screens performed.